Sockeye 1.3 Release Note

Please read this before downloading Sockeye 1.3

Platforms

Linux - We have tested on RedHat 7.2 and 8.0. We have
also run Sockeye on SuSE 8.x Pro, but have tested it less thoroughly on
this OS.

Windows - We have tested on Win2K, and on XP Pro and
Home.

Mac OS X: Please run Sockeye 1.1 using Java Webstast by following this link

Installing on Linux and Windows

Sockeye uses installers built with InstallAnywhere from Zero G
(www.zerog.com).

The download file is executable (install.bin on Linux,
install.exe on Windows). Running it will open an installer that
will let you specify where to install Sockeye, and whether and where to put a
launch link (Linux) or icon (Windows). It will also indicate how much free
disk space you need and how much you have.

On Linux, if you install no links, you will start Sockeye by running the
sockeye shell script in its install directory.

On Windows, if you install an icon on the desktop, you will start Sockeye
by double-clicking on this icon.

Uninstalling

Windows: Sockeye can be removed from: Control panel > Add or Remove
Programs.

Linux or Windows: run the Uninstall_Sockeye_VER script (or .exe)
that is in Sockeye's UninstallerData subdirectory. (VER will be the
version number.)

The uninstaller will only remove the files that it installed, so any files
created after the installation will not be removed. These might include
GFF files copied to .../data/GFF/, or session or sequence files. When the
uninstaller is finished, remove any remaining files or folders manually.

Installed directory structure

Sockeye installs the following directory structure. You can choose the
install_directory.

If you save sequence data from the sequence panel, you may choose
to create a sequences folder under the installation directory.
(You can save sequence data in a different location.)

If you save sessions, you may choose to create a
sessions folder under the installation directory. (You can save
sequence data in a different location.)

If you save both sequences and sessions under the installation directory,
the directory structure will also include -

install_directory

...

sequences - saved sequences (FASTA or TXT)

sessions/MySessionName.../ - session subdirectories and XML
files

...

Java

Sockeye is a Java application. You can download a version that is bundled
with a 'private' Java (VM/JRE)/Java3D that only Sockeye will use, or you can
download a much smaller file that has no bundled Java.

The bundled Java is 1.4.1_01; the bundled Java3D is
1.3.1 beta.

Installer with bundled Java

For most users, this is the simplest, most reliable approach.

You do not need to have Java or Java3D installed outside of
Sockeye in order to run Sockeye. The installer will install the Java that
Sockeye needs.

Download/installation sizes -

Linux - Download: ~ 65 MB. Installed application:
~100 MB.

Windows - Download: ~40 MB. Installed application ~90
MB.

Windows, Java3D, DirectX

For Windows, we offer installers with either DirectX version of
Java3D.

The DirectX version requires a recent version of DirectX (see above
j3d.org link). We have tested Sockeye with Microsoft's current
version of DirectX, 9.0b, on Win2K and XP Pro. You can find the version
installed on your computer by running Start > Run > dxdiag. You
can get the latest DirectX version at
http://www.microsoft.com/windows/directx/default.aspx.

Note that the DirectX version of Java3D does not support
Antialiasing. This is likely only to matter for publication-quality,
exported JPG images.

RAM

We have run Sockeye on PCs with between 192 MB and 1 GB of RAM.

This release allows Sockeye's Java a maximum (heap) of 128 MB RAM, and we
recommend having at least 256 MB installed.

Working with large datasets may require more RAM than this.

We are exploring giving Sockeye more RAM. The online help discusses how
you can change the maximum Java heap size setting by editing the LAX XML file
in the install directory.

Graphics card

Because Sockeye is a 3D application, it demands much more powerful
graphics hardware than a 2D genomic browser.

The more 3D features you display, the more graphics power you will need to
maintain a responsive 3D environment.

The development team works with cards that are at least at the
level of a GeForce2 MX. A card of this level still gives sluggish 3D zooms and
rotations with a display showing, e.g., all 19.5K genes on the C.
elegans genome.